Dear Rachel,
The fact that you are seeing the error:
mpirun: Command not found.
I part of your problem. On IBM Power 4 machines running AIX (I assume you
are running AIX) one typically uses IBM's parallel operating environment
"POE".
You would typically run a parallel job setting:
setenv MP_NODES 1
setenv MP_TASKS_PER_NODE 8
poe $AMBERHOME/exe/sander.MPI -O blah blah blah
poe reads the environment variables to determine the number of cpus to use
rather than using a -np x option like mpirun would.
Thus to run the parallel test cases in amber9 you would set the above
environment variables to the combination of nodes and tasks you want and
then run:
setenv DO_PARALLEL poe
make test.sander.parallel
However, I believe the main issue you are having is with compiling and from
your earlier emails this seemed to be an issue with the mpi installation:
#include file "mpif.h" not found.
This could come from two situations. Firstly IBM's mpi might never have been
installed on your machine or secondly your environment variables might not
be configured correctly.
Try 'which mpxlf90' and see if it returns /usr/bin/mpxlf90
if it says 'mpxlf90: Command not found.' then I suspect mpi is not installed
or possibly installed in a non standard place. Check with whoever setup the
machine to find out which mpi they installed and where.
For the moment you should be able to build and test the serial version. I
would advise you to do this first to make sure things are working. Do:
cd $AMBERHOME/src
./configure -nopar xlf90_aix
make clean
make
cd ../test
make clean
make
All the best
Ross
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| San Diego Supercomputer Center |
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From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
Rachel
Sent: Wednesday, November 22, 2006 02:09
To: amber.scripps.edu
Subject: Re: AMBER: compile amber8 on IBM-sp4
Hi, Scott,
Thanks very much for your reply, however, i am still not clear how to solve
the problem, you suggested to use 'make -n'? and the results are as
following:
----------------------------------------------------------------------
cd dmp; ./Run.dmp
cd adenine; ./Run.adenine
cd cytosine; ./Run.cytosine
cd nonper; ./Run.nonper
cd nonper; ./Run.nonper.belly
cd nonper; ./Run.nonper.belly.mask
cd nonper; ./Run.nonper.min
cd nonper; ./Run.cap
cd nonper; ./Run.nonper.nocut
cd tip4p; ./Run.tip4p
cd tip5p; ./Run.tip5p
cd 4096wat; ./Run.pure_wat
cd dhfr; ./Run.dhfr
cd dhfr; ./Run.dhfr.noshake
cd dhfr; ./Run.dhfr.min
cd gb_rna; ./Run.gbrna
cd gb_rna; ./Run.gbrna.min
cd gb_rna; ./Run.gbrna.ln
cd gbsa_xfin; ./Run.gbsa
cd polarizable_water; ./Run.pol_wat
cd ubiquitin; ./Run.ubiquitin
cd dna_pol; ./Run.dna_pol
cd aspash; ./Run.aspash
cd circ_dna; ./Run.circdna
cd gb2_trx; ./Run.trxox
cd trx; ./Run.trx
cd trx; ./Run.trx.cpln
cd cnstph; ./Run.cnstph
cd rdc; ./Run.dip
cd tgtmd/change_target; ./Run.tgtmd
cd tgtmd/change_target.rms; ./Run.tgtmd
cd tgtmd/change_target.ntr; ./Run.tgtmd
cd tgtmd/conserve_ene; ./Run.tgtmd
cd tgtmd/minimize; ./Run.tgtmin
cd tgtmd/PME; ./Run.tgtPME
cd trajene; ./Run.trajene
cd pheTI; ./Run.0; ./Run.1; ./Run.p0; ./Run.p1
cd ion_wat; ./Run.ion_wat
cd alp; ./Run.alp
cd pb_pgb; ./Run.pbpgb
cd umbrella; ./Run.umbrella
cd LES_noPME; ./Run.LESmd
cd LES_noPME; ./Run.LESmd.rdiel
cd LES; ./Run.PME_LES
cd LES_CUT; ./Run.LES
cd LES_TEMP; ./Run.2temp
cd LES_GB; ./Run.LES
make: 1254-002 Cannot find a rule to create target \ from dependencies.
Stop.
----------------------------------------------------------------------------
----------------------------
As you said the compilation line is broken, how can I make sure i provided
enough details? and if i use 'make test.sander', etc. instead of make
test.parallel, then i got:
----------------------------------------------------------------------------
---------------------------
cd dmp; ./Run.dmp
This test not set up for parallel
cannot run in parallel with #residues < #pes
cd adenine; ./Run.adenine
This test not set up for parallel
cannot run in parallel with #residues < #pes
==============================================================
cd cytosine; ./Run.cytosine
mpirun: Command not found.
./Run.cytosine: Program error
make: 1254-004 The error code from the last command is 1.
----------------------------------------------------------------------------
---------------------------
This is the first time I compile amber myself, and as it is IBM-SP4 machine,
so what i did was just follow Carlos Sosa's Running Amber on IBM systems (
<
http://www.msi.umn.edu/~cpsosa/ChemApps/MolMech/amber/patches/amber8/INSTAL
L_ibm>
http://www.msi.umn.edu/~cpsosa/ChemApps/MolMech/amber/patches/amber8/INSTALL
_ibm) on AMBER website, I really appreciate your help if anyone can let me
know some more details of how to do it.
Best regards,
Rachel
On 11/21/06, Scott Brozell <sbrozell.scripps.edu> wrote:
Hi,
On Tue, 21 Nov 2006, Rachel wrote:
> Dear all,
>
> I am trying to compile amber8 on the IBM-SP4 machines, I used './configure
> -mpi xlf90_aix', after i used 'make paralle', i got the following error
> message:
> "egb.f", line 131.12: 1506-296 (S) #include file "mpif.h" not found.
> make: 1254-004 The error code from the last command is 1.
It looks like the compilation line is broken.
You didn't provide enough detail, so the full command
invoked by make is not clear.
make should be invoking something like, eg
/lib/cpp -traditional -I/usr/lpp/ppe.poe/include -P
-I/usr/local/srb/9/src/include -DMPI -DNMLEQ -DCLINK_PLAIN -Drs6000 -DPOE
sander.f > _sander.f
mpxlf90_r -bmaxdata:0x80000000 -c -qfixed -c -qfree -o sander.o
_sander.f
Compare this with the output of make -n
What happens if you enter mpxlf90_r -show -help ?
> and then if i go to the $AMBERHOME/test directory and use 'make
> test.parallel', it says:
See page 7 errata
http://amber.scripps.edu/doc8/errata.html
Scott
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Received on Wed Nov 22 2006 - 23:01:52 PST
